The aim of the project is to look at the DEGs across different diets in heart as well as Muscle

Final Conclusion The DEG's number (fdr < 0.05 and post prob >=0.5) are 3600, 6300,6405, 8494 genes when raw fold change values multiplied by 10, 50, 100 and 1000. After discussion with prof sujoy, we decided to use raw fold change values multiplied by 10 which is giving enough number of DEG's and also we will encounter will less number of false positives when compared with raw foldchange values multiplied by 50, 100 and 1000

EBSEqHMM timeseries analysis will find out the genes that vary across the time points. It used DESeq2 median normalisation to overcome the differences in the sequencing depths.

Salmon (Transcriptome aligner) generated quantification files (sf files). Gene summarization was done using tximport and then limma was used to find DEG's